GGGenome

GGGenome is a ultrafast DNA sequence search service hosted by Database Center for Life Science (DBCLS). See GGGenome Help for more details.

BioServices.GGGenome is a Julia module interfaces with the GGGenome REST API to query a DNA sequence to various databases programmatically.

Getting Started

Import module:

using BioServices.GGGenome

Available Databases

Genome sequences (hg19, mm10, dm3, ce10, TAIR10, pombe, etc.) and other sequence databases (e.g., refseq) are available.

Full list of available databases can be found at [https://gggenome.dbcls.jp/en/mm10/help.html#db_list].

Examples

Example 1

• Search TTCATTGACAACATT in
• human genome hg19 (default),
• with perfect matches (default),
• in json format.

julia> res = gggsearch("TTCATTGACAACATT", format="bed", output="toString");

julia> print(res)
track name=GGGenome description="GGGenome matches"
chr1    83462475        83462490        .       0       +
chr2    161223114       161223129       .       0       +
chr3    15289789        15289804        .       0       +
chr3    84619844        84619859        .       0       +
....

Example 2

• Search TTCATTGACAACATTGCGT in
• mouse genome mm10,
• allowing 2 mismatches/gaps,
• search for + strand only,
• in tab-delimited txt format.

julia> res = gggsearch("TTCATTGACAACATTGCGT", db="mm10", k=2, strand="+", format="txt", output="toString");

julia> print(res)
# [ GGGenome | 2018-07-01 22:59:01 ]
# database:     Mouse genome, GRCm38/mm10 (Dec, 2011)
# query:        TTCATTGACAACATTGCGT
# count:        41
# name  strand  start   end     snippet snippet_pos     snippet_end
chr1    +       19461997        19462014        AGTTATTCAGCTTTCTATCACGATCAGAGAACAAGCTGAGAAAAGGATGTTTTTGCTTTTGCTTTTGTTTTTCTTCTTATTTTGGAGTTCTCATCCATGATTCATTGACACCATTGCTTTGGCCTCTGGGAAGGGCAGCATATCTGGGTAAAAGCAGATAGCAGAGCAAATCTGCTTACTGCAACCAGCCAGGAAGGAAGCAATGAAAGCACGTTCAC  19461897        19462114
chr1    +       98281503        98281520        TCTAGTGAGGAGAAATGTAAGCTAACGTGATAAACATTGTTTCTGATACACTAATTAAACTGACTTTTGAAAAGATGGCTTACATGTCTATCTAACATGTTTCATTGACACCATTGCTATAGTATGTAATTTTAATGTAAAATAGCCTTCTTTGCAGGGAATCCAGCCTGCTGCTGAATCTTTAAATTTTCAGTGTCTGTTGTCATAGTAACCAGAAT  98281403        98281620
...

Understanding output parameters

By default, gggsearch() returns a HTTP.Messages.Response object.

julia> query = "GTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGA";

julia> res = gggsearch(query, db="refseq", format="txt");

julia> typeof(res)
HTTP.Messages.Response

By setting output="toString", gggsearch() returns a String object.

julia> query = "GTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGA";

julia> res = gggsearch(query, db="refseq", format="txt", output="toString");

julia> typeof(res)
String

julia> println(res)
# [ GGGenome | 2018-07-01 22:25:16 ]
# database:     RefSeq complete RNA release 88 (May, 2018)
# query:        GTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGA
# count:        15
# query:        TCCCGCCGGCTTCTCCGGGATCGGTCGCGTTACCGCAC
# count:        10
# name  strand  start   end     snippet snippet_pos     snippet_end
NR_003279.1 Mus musculus 28S ribosomal RNA (Rn28s1), ribosomal RNA      +       2326    2363    GAAGGGACGGGCGATGGCCTCCGTTGCCCTCGGCCGATCGAAAGGGAGTCGGGTTCAGATCCCCGAATCCGGAGTGGCGGAGATGGGCGCCGCGAGGCCAGTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGAGGCCTCGGGGAGAGTTCTCTTTTCTTTGTGAAGGGCAGGGCGCCCTGGAATGGGTTCGCCCCGAGAGAGGGGCCCGTGCCTTGGAAAGCGTCGCGGTTCC      2226    2463
NR_003287.4 Homo sapiens RNA, 28S ribosomal N5 (RNA28SN5), ribosomal RNA        +       2574    2611    GGGACGGGCGATGGCCTCCGTTGCCCTCGGCCGATCGAAAGGGAGTCGGGTTCAGATCCCCGAATCCGGAGTGGCGGAGATGGGCGCCGCGAGGCGTCCAGTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGTTCTCTTTTCTTTGTGAAGGGCAGGGCGCCCTGGAATGGGTTCGCCCCGAGAGAGGGGCCCGTGCCTTGGAAAGCGTCGCGGTTCCG      2474    2711
...

By setting output="extractTopHit", gggsearch() returns a String object containing the top hit. Currently, this only works with format="txt".

julia> query = "GTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGA";

julia> res = gggsearch(query, db="refseq", format="txt", output="extractTopHit");

julia> typeof(res)
String

julia> println(res)
NR_003279.1 Mus musculus 28S ribosomal RNA (Rn28s1), ribosomal RNA      +       2326    2363    GAAGGGACGGGCGATGGCCTCCGTTGCCCTCGGCCGATCGAAAGGGAGTCGGGTTCAGATCCCCGAATCCGGAGTGGCGGAGATGGGCGCCGCGAGGCCAGTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGAGGCCTCGGGGAGAGTTCTCTTTTCTTTGTGAAGGGCAGGGCGCCCTGGAATGGGTTCGCCCCGAGAGAGGGGCCCGTGCCTTGGAAAGCGTCGCGGTTCC      2226    2463

Methods

gggsearch(query::AbstractString; 
          db="hg19", k=0, strand=nothing, 
          format="html", timeout=5, 
          output=nothing, show_url=false)

gggdbs()